Introduction
< Explain >
Goals
< what are you trying to achieve >
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Learn how to communicate with cbioportal and study what is
available.
- This portal is hierarchically structured. This is the workflow.
- Initiate cBioPortal API
- List studies
- List available datasets for the chosen study
- Find all sample IDs associated with the dataset
- Acquire clinical data
- List available molecular data associated with the dataset
- Download
Find you TCGA ID
- Important here: you need to replace this with your own assigned TCGA
ID. For this report I’m using TCGA-AR-A24T
Clinical data.
Now that we have a basic understanding of what is available lets go
and download the actual data.
mutation table
Identifying pathogenic mutations. <— need to redo with mt from
here onwards
Now that the data has been succesfully donwloaded and annotated lets
study it a bit more.